Theses
Date of Award
Spring 5-30-2024
Document Type
Thesis
Degree Name
Master of Science (MS)
Department
Biological Sciences
First Advisor
Lindsay Lafave, PhD
Second Advisor
Kristina Ames, PhD
Third Advisor
Stephen M. Redenti, PhD
Fourth Advisor
Haiping Cheng, PhD
Abstract
Lung adenocarcinoma (LUAD) is the most common form of non-small cell lung cancer in the United States and is a major cause of cancer-related mortality. Patients with LUAD experience severe pulmonary symptoms and often progress to metastatic disease. Our previous work has shown that LUAD cells downregulate lung cell identity programs across cancer progression such as genes involved in the maintenance of epithelial barrier integrity. For example, CFTR (Cystic Fibrosis Transmembrane Conductance Regulator), a water and bicarbonate channel, is expressed in normal alveolar type 2 (AT2) cells and is downregulated in cells that give rise to LUAD. Although the loss of CFTR expression is linked to LUAD, the exact mechanism responsible for changes in lung cell fate and lung cancer progression remain elusive. Here, we investigate the role of CFTR in LUAD progression, revealing epigenomic and transcriptomic factors affecting CFTR activity. We hypothesize that the downregulation of CFTR activity disrupts chromatin-mediated processes responsible for preserving the expression of genes associated with AT2 identity and thus, leads to LUAD. To analyze CFTR expression in AT2 cells across diverse growth environments, we used quantitative PCR (qPCR) and accessed cells grown in 2D cultures (flat growth), 3DMatrigel domes (variable nutrient access), and 3D Celvivo bioreactor (uniform nutrient access). Our data shows that compared to the cells grown in 2D, the 3D environment increased CFTR activity, highlighting the interplay between environmental factors and Cftr expression. Moreover, a decrease in Cftr expression was linked to alterations in AT2-related gene expression, such as reduction of lung identity markers Nkx2.1, Aqp3, and Aqp5. To investigate CFTR activation in alveolar cells during LUAD progression, we utilized our mouse model with the KRasG12D oncogenic mutation and deletion of the Trp53 gene. Our mouse model revealed the presence of diverse cell states, including a CFTR high population which co-expressed AT2 identity markers Nkx2.1 and Aqp3. Our data underscores the interplay between Cftr expression, AT2 cellular identity and LUAD progression. We have optimized a novel method to culture AT2-derived cells in a Celvivo bioreactor, simulating organism-level nutrient exchange. We also assessed the impact of CFTR knockouts (KOs) in Calu3, an airway LUAD cell line, on water channels and transcription factors associated with alveolar cell identity, revealing that CFTR KO did not lead to significant alterations in the expression levels. However, ATAC-seq analysis unveiled distinct changes in chromatin accessibility associated with CFTR KO, particularly affecting specific genomic regions such as ZNF134, NFYB, and NRF1, which displayed significant alterations in chromatin accessibility in control and compared to CFTR KO cells, suggesting a potential regulatory role of CFTR activity on chromatin state in lung cells. These findings shed light on the intricate interplay between CFTR, AT2 cellular identity, and LUAD progression, offering insights into potential therapeutic strategies aimed at restoring CFTR activity.
Recommended Citation
Vallejo Alvarez, Marilyn G., "Effect of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Loss in Lung Adenocarcinoma (LUAD)" (2024). CUNY Academic Works.
https://academicworks.cuny.edu/le_etds/36